Hello all, I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the minimization, equilibration, and production runs given. Then I copied the 10ns production run .gro to a different folder so that I can run it with charmm36-nov2016.ff instead of the ff given.
When running the command "gmx_mpi pdb2gmx -ff charmm36-nov2016 -f old_membrane_lipid_only.pdb -o old_membrane_pdb2gmx.pdb -p topol.top -water tip3p" it generates a very large .top file (26.8 MB) that has [ atoms ] and perhaps other headings. I was under the impression that the .top should have been small and just contained the include line for where the POPE and POPG .itps were in the charmm36-nov2016. Did I do something wrong? Would this give me a simulation that isn't accurate? Command Notes: http://pastebin.com/raw/TC0L1H4K topol.top (26.8 MB): https://ufile.io/5897d2 Thank you again for all your help, it is very much appreciated :) - Jonathan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
